Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,816,244 T→C 7.8% pseudogene (306/669 nt) rph ← ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,816,2440TC 7.8% 151.2 / 4.0 51pseudogene (306/669 nt)rphribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
Reads supporting (aligned to +/- strand):  ref base T (23/24);  new base C (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CACCAGCTTCTGTAGCGCATCTACCAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTG  >  NC_000913/3816115‑3816384
                                                                                                                                 |                                                                                                                                            
caccaGCTTCTGTAGCGCATCTACCAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGc                                                                                                                             <  6:221594/147‑1 (MQ=255)
    aGCTTCTGTAGCGCATCTACCAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACggg                                                                                                                        <  3:269166/148‑1 (MQ=255)
        tCTGTAGCGCATCTACCAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGAt                                                                                                                    >  8:122180/1‑148 (MQ=255)
          tGTAGCGCATCTACCAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGAt                                                                                                                    >  1:375568/1‑146 (MQ=255)
                    cTACCAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGAt                                                                                                        >  7:284512/1‑148 (MQ=255)
                       ccAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGAtt                                                                                                       <  7:19480/146‑1 (MQ=255)
                       ccAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTc                                                                                                     <  7:122180/148‑1 (MQ=255)
                               aCGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGc                                                                                             >  1:318323/1‑148 (MQ=255)
                                 gCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGt                                                                                           >  6:3208/1‑148 (MQ=255)
                                     gCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCAtt                                                                                                 <  6:328505/138‑1 (MQ=255)
                                     gCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCAtt                                                                                                 >  5:328505/1‑138 (MQ=255)
                                     gCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCAc                                                                                       <  5:3208/148‑1 (MQ=255)
                                      cACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCg                                                                                            >  6:71176/1‑142 (MQ=255)
                                      cACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCg                                                                                            <  5:71176/142‑1 (MQ=255)
                                       aCCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCt                                                                                                                                              <  5:169128/91‑1 (MQ=255)
                                       aCCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCt                                                                                                                                              >  6:169128/1‑91 (MQ=255)
                                             aaTCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTa                                                                               >  7:391329/1‑148 (MQ=255)
                                                  aCGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCttt                                                                          >  3:360500/1‑148 (MQ=255)
                                                   cgcgGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTc                                                                         >  2:54841/1‑148 (MQ=255)
                                                           gcgTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTc                                                                 <  2:318323/148‑1 (MQ=255)
                                                                ccaccaTCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGa                                                             <  5:350725/147‑1 (MQ=255)
                                                                  accaTCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCg                                                          >  1:68023/1‑148 (MQ=255)
                                                                    caTCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGtt                                                        <  1:363399/148‑1 (MQ=255)
                                                                    caTCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGtt                                                        <  1:54841/148‑1 (MQ=255)
                                                                    caTCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGtt                                                        <  2:68023/148‑1 (MQ=255)
                                                                         gCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCAACCTGCTTACCTTTCGCCGCTTCACGATCGTTACtgg                                                   >  8:78773/1‑148 (MQ=255)
                                                                             gAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGtgtg                                               >  5:18625/1‑148 (MQ=255)
                                                                                 cACGTCGCAGTCCAGCGTAATGGTGAACTCACCCTGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTa                                           <  7:78773/148‑1 (MQ=255)
                                                                                    gTCGCAGTCAAGCGTAATGGTTAACTCACCCAGAGCTTTCAAATCTACTGCCGCGCGAATAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCAcc                                                                                      >  3:186875/1‑102 (MQ=255)
                                                                                      cGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAAc                                       <  5:136210/147‑1 (MQ=255)
                                                                                      cGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAAc                                       >  6:136210/1‑147 (MQ=255)
                                                                                       gCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGt                                     <  4:360500/148‑1 (MQ=255)
                                                                                           tCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGgc                                  <  5:319287/147‑1 (MQ=255)
                                                                                            ccAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGtt                                                        <  8:100810/124‑1 (MQ=255)
                                                                                            ccAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGtt                                                        >  7:100810/1‑124 (MQ=255)
                                                                                            ccAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTgg                                   >  6:319287/1‑145 (MQ=255)
                                                                                            ccAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGgcag                                >  3:104559/1‑148 (MQ=255)
                                                                                                cGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTcc                                                                                         >  6:282001/1‑87 (MQ=255)
                                                                                                cGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTcc                                                                                         <  5:282001/87‑1 (MQ=255)
                                                                                                    aTGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGt                        <  8:284512/148‑1 (MQ=255)
                                                                                                        tGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGt                        <  1:303479/144‑1 (MQ=255)
                                                                                                        tGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGt                        >  2:303479/1‑144 (MQ=255)
                                                                                                              cACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGt              >  8:18217/1‑148 (MQ=255)
                                                                                                              cACCCAGCGCTTTCAAATCCACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAg                                                            <  6:242480/102‑1 (MQ=255)
                                                                                                              cACCCAGCGCTTTCAAATCCACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAg                                                            <  6:236841/102‑1 (MQ=255)
                                                                                                              cACCCAGCGCTTTCAAATCCACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAg                                                            >  5:236841/1‑102 (MQ=255)
                                                                                                              cACCCAGCGCTTTCAAATCCACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAg                                                            >  5:242480/1‑102 (MQ=255)
                                                                                                                 ccAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGAt           <  8:391329/148‑1 (MQ=255)
                                                                                                                  cAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATc          <  6:18625/148‑1 (MQ=255)
                                                                                                                         ttCAAATCTCCTGCCGCCCCAAGCGCCCGGGCGAGCCGACGCTGGATTTCCCTGGTGCGGCCACCCTGCTTACCTCTCGCCGCTGCACGAGCGTTACGGGTGTGGGTCCCACGTGGCAGCATGCCGCACTCTGCGGCGATCCAgccct   <  4:104559/148‑1 (MQ=255)
                                                                                                                          tCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAgccctg  >  4:172985/1‑148 (MQ=255)
                                                                                                                                cTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGc                 >  4:74195/1‑127 (MQ=255)
                                                                                                                                cTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGc                 <  3:74195/127‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                            
CACCAGCTTCTGTAGCGCATCTACCAGCGCCACGCAGGCACCCGTAATCGACGCGGTACGCGTGCCACCATCAGCCTGAAGCACGTCGCAGTCCAGCGTAATGGTGAACTCACCCAGCGCTTTCAAATCTACTGCCGCGCGAAGAGCACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTG  >  NC_000913/3816115‑3816384

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑